"Added more comments to the program"

import java.io.File;

import java.util.ArrayList;

/**************************************************************************

 * Main for tarantula calculation, takes 2 command line arguments

 * arg[1] - compact-cov-matrix.json file

 * arg[2] - package.name of test program

 * examples of the args are in comments next to the args indexes below 

 **************************************************************************/

public class TarantulaMain {

	    public static void main(String[] args) throws ClassNotFoundException {

	        // create the Matrix Reader to get Test -- Stmt information

	        File f = new File(args[0]); // "/abs/path/to/triangle-mvn-compact-cov-matrix.json"*

		 reader = new covMatrixReader(f);

	        File f = new File(args[0]); // example: "/homes/iws/kevinb22/Downloads/triangle-mvn-compact-cov-matrix.json"

	        covMatrixReader reader = new covMatrixReader(f);

	        // The test count is a Long in the Json file, must parse it to an Integer

	        Long testCountLong = reader.getTestCount();

	        String testCountString = testCountLong.toString();

	        int testCountInt = Integer.parseInt(testCountString);

	        // create Runner class to get the failing cases from JUnit tests

	        Class testClass = Class.forName(args[1]); //"TarantulaCalculator.TriangleTest"

	        Class testClass = Class.forName(args[1]); // example: "TarantulaCalculator.TriangleTest"

	        Runner r = new Runner(testClass);

	        r.determineFailCases();

	        ArrayList<Integer> fails = r.getFailCases();

	        boolean[] F =new boolean[testCountInt];

	        Arrays.fill(F, false); 

	        for(Integer i : fails) {

	            F[i - 1] = true;

	            F[i - 1] = true; //true=failing test

	        }

	        calc.setF(F);

	        // set live test cases -- [test]

	        // by default all test cases are used

	        boolean[] L = new boolean[testCountInt];

	        Arrays.fill(L, true);

	        calc.setL(L);

	        // calc will perform all the calculations

	        calc.compute();

	        //display the results

	        System.out.println("For program: " + reader.getFullName());

	        displayConf(calc.getConfidence(), reader.getFirstLine());

	        System.out.println("------------------------------------------------------------------");

	        displaySusp(calc.getSuspiciousness(), reader.getFirstLine());

	    }

	    // display the confidence array for the program	     

	    // displays the confidence per line of the program starting from the

	    // first line of the program identified by tacoco

	    public static void displayConf(double[] a, Long firstLine){

	        System.out.println("Confidence Array");

	        for(int i = 0; i < a.length; i++) {

	        }

	    }

	    // dispaly the susp. array for the program

	    // displays the suspicion per line of the program starting from the

	    // first line of the program identified by tacoco

	    public static void displaySusp(double[] a, Long firstLine){

	        System.out.println("Suspicion Array");

	        for(int i = 0; i < a.length; i++) {